This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Phosphatidylglycerol (PG) is the major phospholipid of plant chloroplasts. PG from Arabidopsis thaliana has an unusual fatty acyl chain, 3,4-trans-hexdecenoyl (D316:1) in the sn-2 position of the major 18:3/D316:1-PG species, as well as in 18:2/D316:1-PG and 16:0/ D316:1-PG. Upon low-energy collisionally activated dissociation (CAD) in a tandem quadrupole or in an ion-trap mass spectrometer, the [M - H][unreadable]ions of the PG molecules, containing D316:1-PG give product-ion spectra that are readily distinguishable from those arising from PGs without the D316:1 species. The D316:1-fatty acid-containing PGs are characterized by MS2 product-ion mass spectra that contain predominant [M - H - 236][unreadable], ions arising from loss of the D316:1-fatty acid substituent as a ketene. This is attributable to the fact that the [unreadable]-hydrogen of the D316:1-fatty acid substituent involved in the ketene loss is an allylic hydrogen, which is very labile. This leads to preferential neutral loss of 236 and provides a sensitive tandem quadrupole mass spectrometric means to identify D316:1-containing PG species in lipid mixtures. The low-energy tandem mass spectrometric approach also permits the structures of the Arabidopsis PGs that consist of two isomeric structures to be unveiled.